Flexibility of the nascent polypeptide chain within the ribosome--contacts from the peptide N-terminus to a specific region of the 30S subunit - PubMed (original) (raw)
Flexibility of the nascent polypeptide chain within the ribosome--contacts from the peptide N-terminus to a specific region of the 30S subunit
K M Choi et al. Eur J Biochem. 1998.
Free article
Abstract
The ribosomal environment of the N-terminus of the nascent polypeptide chain has been investigated using peptides of different lengths, synthesized in situ on Escherichia coli ribosomes; the peptides each carry a photoreactive diazirine moiety at their N-terminus, so as to generate cross-links to neighbouring ribosomal components. Our previous studies [Choi, K. M. & Brimacombe, R. (1998) Nucleic Acids Res. 26, 887-895] with three independent families of peptides, derived from the E. coli ompA protein gene, the tetracycline-resistance gene and the bacteriophage T4 gene 60, identified a series of sites within the 23S rRNA to which the peptides became cross-linked. The distribution of these cross-links indicated that the nascent peptide is very flexible within the 50S subunit. Here, we demonstrate that the N-termini of the ompA and gene-60 peptides can, in addition, even become concomitantly cross-linked to the 30S subunit. The cross-linking is predominantly to 30S ribosomal proteins S1, S2, S4 and (to a lesser extent) S3, which form a cluster near to the decoding region. This result is discussed in terms of the flexibility of the nascent peptide during the co-translational folding process, and in terms of the 'ribosomal bypass' phenomenon which is known to occur during translation of the gene 60 mRNA.
Similar articles
- The path of the growing peptide chain through the 23S rRNA in the 50S ribosomal subunit; a comparative cross-linking study with three different peptide families.
Choi KM, Brimacombe R. Choi KM, et al. Nucleic Acids Res. 1998 Feb 15;26(4):887-95. doi: 10.1093/nar/26.4.887. Nucleic Acids Res. 1998. PMID: 9461444 Free PMC article. - Mapping the path of the nascent peptide chain through the 23S RNA in the 50S ribosomal subunit.
Stade K, Jünke N, Brimacombe R. Stade K, et al. Nucleic Acids Res. 1995 Jul 11;23(13):2371-80. doi: 10.1093/nar/23.13.2371. Nucleic Acids Res. 1995. PMID: 7630714 Free PMC article. - The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.
Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, Wöhnert J, Görlach M, van Heel M, Brimacombe R. Mueller F, et al. J Mol Biol. 2000 Apr 21;298(1):35-59. doi: 10.1006/jmbi.2000.3635. J Mol Biol. 2000. PMID: 10756104 - Cotranslational folding of nascent proteins on Escherichia coli ribosomes.
Hardesty B, Kudlicki W, Odom OW, Zhang T, McCarthy D, Kramer G. Hardesty B, et al. Biochem Cell Biol. 1995 Nov-Dec;73(11-12):1199-207. doi: 10.1139/o95-129. Biochem Cell Biol. 1995. PMID: 8722037 Review. - Mechanism of ribosome assisted protein folding: a new insight into rRNA functions.
Samanta D, Das A, Bhattacharya A, Basu A, Das D, DasGupta C. Samanta D, et al. Biochem Biophys Res Commun. 2009 Jun 26;384(2):137-40. doi: 10.1016/j.bbrc.2009.04.106. Epub 2009 May 3. Biochem Biophys Res Commun. 2009. PMID: 19401192 Review.
Cited by
- Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing.
Todd GC, Walter NG. Todd GC, et al. RNA. 2013 May;19(5):685-700. doi: 10.1261/rna.037291.112. Epub 2013 Mar 14. RNA. 2013. PMID: 23492219 Free PMC article. - Polytopic membrane protein folding at L17 in the ribosome tunnel initiates cyclical changes at the translocon.
Lin PJ, Jongsma CG, Pool MR, Johnson AE. Lin PJ, et al. J Cell Biol. 2011 Oct 3;195(1):55-70. doi: 10.1083/jcb.201103118. Epub 2011 Sep 26. J Cell Biol. 2011. PMID: 21949410 Free PMC article. - Birth, life and death of nascent polypeptide chains.
Jha S, Komar AA. Jha S, et al. Biotechnol J. 2011 Jun;6(6):623-40. doi: 10.1002/biot.201000327. Epub 2011 Apr 29. Biotechnol J. 2011. PMID: 21538896 Free PMC article. Review. - Confined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions.
Ellis JP, Culviner PH, Cavagnero S. Ellis JP, et al. Protein Sci. 2009 Oct;18(10):2003-15. doi: 10.1002/pro.196. Protein Sci. 2009. PMID: 19569194 Free PMC article. - Protein folding by domain V of Escherichia coli 23S rRNA: specificity of RNA-protein interactions.
Samanta D, Mukhopadhyay D, Chowdhury S, Ghosh J, Pal S, Basu A, Bhattacharya A, Das A, Das D, DasGupta C. Samanta D, et al. J Bacteriol. 2008 May;190(9):3344-52. doi: 10.1128/JB.01800-07. Epub 2008 Feb 29. J Bacteriol. 2008. PMID: 18310328 Free PMC article.